DECODING THE IMPACT OF TRANSPOSABLE ELEMENTS ON GENE REGULATION

描述(由申请人提供)： 至少一半的人类基因组来自转座元件(TES)。这些高度重复的元件通常含有转录因子结合位点和表观遗传调控信号。TES在进化过程中形成了基因调控网络，在疾病中往往处于失调状态。然而，TE序列对功能调控网络的贡献程度以及TE序列如何从寄生DNA进化到功能元件仍不清楚。回答这些问题将通过包括TES对全基因组基因调控模式的贡献来扩大我们对调控网络的理解。在这项建议中，我们引入了一种新的策略，将TE衍生的细胞类型特异性增强子的计算预测与大规模平行的报告基因分析相结合，以了解TE对细胞类型特异性基因调控的影响。在具体目标1中，我们计划开发一种基于表观基因组学的方法来检测TE衍生的增强子及其靶基因。然后，我们将使用CRE-seq，一种大规模的平行报告基因分析来测试它们的调控活性。我们将利用计算模型来预测TE衍生的增强剂。如果成功，我们不仅将产生最大的TE来源的细胞类型特异性增强子目录，而且我们还将创建一个强大的框架，用于检测TES对任何细胞类型或组织中的基因调控的贡献。在特定目标2中，我们将开发一种系统发育信息的功能关联分析。我们将重建代表候选TES进化中间产物的序列，并用Cre-seq测试这些序列的调节活性。我们将解决的问题包括：特定类别的TES是否获得了Tf结合位点，然后迅速传播，或者TES是否首先传播，然后获得Tf结合位点。如果成功，我们将了解哪些序列特征驱动TES的功能潜力，以及不同TES家族在调控网络进化过程中遵循的进化模式。这样的理解将极大地改善我们对基因调控网络进化的图景，包括TES的影响，TES是一类快速进化的调控序列，在功能基因组学研究中基本上被忽视。该提案中开发的方法将对诸如ENCODE、路线图表观基因组学、TCGA和其他大型基因组学项目等财团产生的数据的使用产生很大影响，这些项目目前从其数据中丢弃了大多数TE衍生序列。这样的改进将反过来加速研究，以了解TES‘对正常基因调控和人类疾病的影响。

DESCRIPTION (provided by applicant): At least half of the human genome is derived from transposable elements (TEs). These highly repetitive elements often harbor transcription factor binding sites and epigenetic regulatory signals. TEs have shaped gene regulatory networks during evolution and are often dysregulated in diseases. However, the extent to which TEs contribute sequences to functional regulatory networks, and how TE sequences evolved from parasitic DNA to functional elements, remains unclear. Answering these questions will expand our understanding of regulatory networks by including the contributions of TEs to genome-wide patterns of gene regulation. In this proposal, we introduce a novel strategy that combines computational prediction of TE derived cell type-specific enhancers with massively parallel reporter gene assays to understand the impact of TEs to cell type-specific gene regulation. In Specific Aim 1 we plan to develop an epigenomics-based approach to detect TE-derived enhancers and their target genes. We will then test their regulatory activities using CRE-seq, a massive parallel reporter gene assay. We will bring to bear computational models that allow us to predict TE-derived enhancers. If successful, not only will we produce the largest catalog of TE-derived cell type-specific enhancers, but also we will have created a robust framework for detecting the contributions of TEs to gene regulation in any cell type or tissue. In Specific Aim 2 we will develop a phylogenetically informed functional association assay. We will reconstruct sequences representing the evolutionary intermediates of candidate TEs and test the regulatory activities of these sequences with CRE-seq. We will address questions including whether particular classes of TEs gained TF-binding sites and then spread quickly, or whether TEs first spread and later gained TF binding sites. If successful, we will develop an understanding of what sequence features drive the functional potential of TEs, and the modes of evolution followed by different families of TEs during regulatory network evolution. Such an understanding will dramatically improve our picture of gene regulatory network evolution by including the effects of TEs, a major class of fast evolving regulatory sequences that have been largely ignored in functional genomics studies. The methods developed in this proposal will have a high impact on the utility of data produced by consortia such as ENCODE, Roadmap Epigenomics, TCGA, and other large- scale genomics projects, which currently discard most TE derived sequences from their data. Such improvement will in turn accelerate research into understanding the impact of TEs' on normal gene regulation and in human diseases.